Twice now I've been playing with this and some other mods. A good while into both colonies I've had an issue where I've lost control of my colony. Both times I tried loading autosaves and both times saves where I had a ship on another world tile the colonists on that tile load fine but my main colony is still lost with all hands. The only common denominator I can think of is that both times the game broke like this is I had just researched and built the Mk.III Phoenix :/ Also the phoenix was in the other world tile both times my main colony was lost but not my caravan.
Lost a lot of time spent on these playthroughs so I'm really bummed about this happening twice now.

Don't know if it will help but here's the log after loading the broken save.
Google Drive link[drive.google.com]

EDIT: I just went back through some older saves from the first playthrough and the oldest couple of saves work as intended and in those I've got an SRAF and in the later ones an albatross but when loading a save where I have a Phoenix it breaks.